grower_prep.cc File Reference

#include <devel/init.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/sequence/SWAligner.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/SimpleScoringScheme.hh>
#include <core/sequence/SequenceAlignment.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/FragmentIO.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <basic/Tracer.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <protocols/hybridization/util.hh>
#include <fstream>
#include <string>
#include <protocols/loops/Loop.hh>

Functions
utility::vector1< protocols::loops::Loop >	get_unaligned (core::id::SequenceMapping const &sequencemap)
void	Prepare ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("grower_prep")

Function Documentation

get_unaligned()

utility::vector1<protocols::loops::Loop> get_unaligned

(

core::id::SequenceMapping const &

sequencemap

)

References basic::options::OptionKeys::cluster::loops.

Referenced by Prepare().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, test.T009_Exceptions::e, basic::init(), NEW_OPT, kic_runner::pdb, and Prepare().

Prepare()

void Prepare

(

)

References utility::options::OptionKeys::options::exit, in::file::fasta(), basic::options::OptionKeys::frags::frag_sizes, basic::options::OptionKeys::in::path::fragments, get_unaligned(), create_a3b_hbs::i, create_a3b_hbs::ii, enumerate_junctions::int, create_a3b_hbs::j, option, lactamize::outfile, kic_runner::pdb, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, runtime_assert, beta_sc_scan::seq, basic::options::OptionKeys::relax::sequence, ObjexxFCL::size(), challenge::ss, basic::options::OptionKeys::cutoutdomain::start, utility::to_string(), TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("grower_prep") ( "grower_prep"  )

static

Referenced by Prepare().